A novel satellite DNA called msDNA (multicopy single-stranded DNA) was originally found in Myxococcus xanthus, a Gram-negative bacterium living in soil (1). It consists of a 162-base single-stranded DNA, the 5' end of which is linked to a branched RNA (msdRNA) of 77 bases by a 2',5'-phosphodiester linkage at the 2' position of the 20th rG residue (2). There are approximately 700 copies of msDNA per genome. msDNA is widely distributed among various myxobacteria including the closely related Stigmatella aurantiaca which possesses an msDNA, msDNA-Sa163. This molecule is highly homologous to msDNA-Mx162 from M. xanthus (3, 4). It is noteworthy that several M. xanthus strains, independently isolated from different sites, all contain msDNA (5). Recently it was found that M. xanthus contains another smaller species of msDNA called msDNA-Mx65 (6). In contrast to the close homology between msDNA-Mx162 and msDNA-Sa163, there is no primary sequence homology between msDNA-Mx162 and the small molecule, msDNA-Mx65. However, it was found that msDNA-Mx65 does share key secondary structures such as a branched rG residue, a DNA-RNA hybrid at the 3' ends of the msDNA and msdRNA, and stem-loop structures in RNA and DNA strands.
It has been further shown that msdRNA is derived from a much longer precursor RNA (pre-msdRNA), which can form a very stable stem-and-loop structure (2). A novel mechanism for msDNA synthesis was proposed, in which the stem-and-loop structure of pre-msdRNA serves as a primer for initiating msDNA synthesis as well as a template to form the branched RNA-linked msDNA, and predicted that a reverse transcriptase (RT) is required for this reaction (2).
Initial studies indicated that msDNA is not found in the common E. coli K-12 laboratory strain (1). To date, it has been observed that approximately 6% of all E. coli isolates from clinical strains carry an msDNA synthesizing system. This synthesizing system has been classified as a retron on the basis of rather surprising similarities between the msDNA and retroviruses and retrotransposons (8).
The present invention provides for an E. coli msDNA synthesizing system. The invention also provides for its products and uses.